John is an Alpha, Sherlock is an Omega. Whether they are bonded or just secretly in love and pining for each other (pre- or unrequited is fine, too) is up to you. It doesn't matter. John is very protective of Sherlock, and he can see that this whole mess with Moriarty is taking its toll on Sherlock, especially given that Moriarty has been quiet for some time.

John decides to investigate on his own, though he probably has to go to Mycroft for help. He wants to deal with it once and for all even if it robs Sherlock of a case of his life. His safety is more important to John.

So, after some time and some help from Mycroft, John finds some quiet, nice house/flat with information that Jim could be there. John enters with a gun drawn. There's a nursery, freshly decorated and furnished, with a baby cot and shelves stack with toys, nappies and such. Among all of this there's Moriarty himself, heavily pregnant.

What John does about this situation is entirely up to you. I'd be happy to see his reaction, moral dilemma and such. Maybe he ends up getting Jim arrested, but makes sure the baby is taken care of when it's born. Really, whatever you come up with is good for me, though I prefer John to stay in character.